From a4449fb6ff038574ddb2cb8d89a411fbebee6d65 Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Mon, 6 May 2024 16:44:45 -0600 Subject: [PATCH] modified doc page, added examples --- doc/src/replicate.rst | 170 +++-- examples/README | 1 + examples/replicate/README | 23 + examples/replicate/data.bond.x | 22 + examples/replicate/data.bond.x.noloop | 21 + examples/replicate/data.bond.x.y | 43 ++ examples/replicate/data.bond.xy | 22 + examples/replicate/in.replicate.bond.x | 34 + examples/replicate/in.replicate.bond.x.noloop | 34 + examples/replicate/in.replicate.bond.x.y | 34 + examples/replicate/in.replicate.bond.xy | 34 + .../{in.replicate => in.replicate.cnt} | 2 +- .../log.6May24.replicate.bond.x.g++.1 | 125 ++++ .../log.6May24.replicate.bond.x.g++.4 | 126 ++++ .../log.6May24.replicate.bond.x.noloop.g++.1 | 121 ++++ .../log.6May24.replicate.bond.x.noloop.g++.4 | 122 ++++ .../log.6May24.replicate.bond.x.y.g++.1 | 125 ++++ .../log.6May24.replicate.bond.x.y.g++.4 | 126 ++++ .../log.6May24.replicate.bond.xy.g++.1 | 125 ++++ .../log.6May24.replicate.bond.xy.g++.4 | 126 ++++ ...e.g++.1 => log.6May24.replicate.cnt.g++.1} | 48 +- ...e.g++.4 => log.6May24.replicate.cnt.g++.4} | 49 +- src/replicate.cpp | 625 ++++++++++++++++-- src/replicate.h | 20 +- 24 files changed, 2015 insertions(+), 163 deletions(-) create mode 100644 examples/replicate/README create mode 100644 examples/replicate/data.bond.x create mode 100644 examples/replicate/data.bond.x.noloop create mode 100644 examples/replicate/data.bond.x.y create mode 100644 examples/replicate/data.bond.xy create mode 100644 examples/replicate/in.replicate.bond.x create mode 100644 examples/replicate/in.replicate.bond.x.noloop create mode 100644 examples/replicate/in.replicate.bond.x.y create mode 100644 examples/replicate/in.replicate.bond.xy rename examples/replicate/{in.replicate => in.replicate.cnt} (94%) create mode 100644 examples/replicate/log.6May24.replicate.bond.x.g++.1 create mode 100644 examples/replicate/log.6May24.replicate.bond.x.g++.4 create mode 100644 examples/replicate/log.6May24.replicate.bond.x.noloop.g++.1 create mode 100644 examples/replicate/log.6May24.replicate.bond.x.noloop.g++.4 create mode 100644 examples/replicate/log.6May24.replicate.bond.x.y.g++.1 create mode 100644 examples/replicate/log.6May24.replicate.bond.x.y.g++.4 create mode 100644 examples/replicate/log.6May24.replicate.bond.xy.g++.1 create mode 100644 examples/replicate/log.6May24.replicate.bond.xy.g++.4 rename examples/replicate/{log.7Jan22.replicate.g++.1 => log.6May24.replicate.cnt.g++.1} (67%) rename examples/replicate/{log.7Jan22.replicate.g++.4 => log.6May24.replicate.cnt.g++.4} (65%) diff --git a/doc/src/replicate.rst b/doc/src/replicate.rst index cea38e1af0..64d87e525a 100644 --- a/doc/src/replicate.rst +++ b/doc/src/replicate.rst @@ -8,113 +8,149 @@ Syntax .. code-block:: LAMMPS - replicate nx ny nz *keyword* + replicate nx ny nz *keyword* ... nx,ny,nz = replication factors in each dimension -* optional *keyword* = *bbox* or *bondlist* +* zero or more keywords may be appended +* keyword = *bbox* or *bond/periodic* .. parsed-literal:: *bbox* = only check atoms in replicas that overlap with a processor's subdomain - *bondlist* = use a generalized algorithm that correctly replicates periodic loops + *bond/periodic* = use a different algorithm that correctly replicates periodic bond loops Examples """""""" -For an example of replicating periodically looped carbon nanotubes, see examples/replicate. +For examples of replicating simple linear polymer chains (periodic or +non-periodic) or periodic carbon nanotubes, see examples/replicate. .. code-block:: LAMMPS replicate 2 3 2 + replicate 2 3 2 bbox + replicate 2 3 2 bond/periodic Description """"""""""" -Replicate the current simulation one or more times in each dimension. -For example, replication factors of 2,2,2 will create a simulation -with 8x as many atoms by doubling the simulation domain in each -dimension. A replication factor of 1 in a dimension leaves the -simulation domain unchanged. When the new simulation box is created -it is also partitioned into a regular 3d grid of rectangular bricks, -one per processor, based on the number of processors being used and -the settings of the :doc:`processors ` command. The -partitioning can later be changed by the :doc:`balance ` or -:doc:`fix balance ` commands. +Replicate the current system one or more times in each dimension. For +example, replication factors of 2,2,2 will create a simulation with 8x +as many atoms by doubling the size of the simulation box in each +dimension. A replication factor of 1 leaves the simulation domain +unchanged in that dimension. -All properties of the atoms are replicated, including their -velocities, which may or may not be desirable. New atom IDs are -assigned to new atoms, as are molecule IDs. Bonds and other topology -interactions are created between pairs of new atoms as well as between -old and new atoms. This is done by using the image flag for each atom -to "unwrap" it out of the periodic box before replicating it. +When the new simulation box is created it is partitioned into a +regular 3d grid of rectangular bricks, one per processor, based on the +number of processors being used and the settings of the +:doc:`processors ` command. The partitioning can be +changed by subsequent :doc:`balance ` or :doc:`fix balance +` commands. -This means that any molecular bond you specify in the original data -file that crosses a periodic boundary should be between two atoms with -image flags that differ by 1. This will allow the bond to be -unwrapped appropriately. - -The optional keyword *bbox* uses a bounding box to only check atoms in -replicas that overlap with a processor's subdomain when assigning -atoms to processors. It typically results in a substantial speedup -when using the replicate command on a large number of processors. It -does require temporary use of more memory, specifically that each -processor can store all atoms in the entire system before it is -replicated. - -The optional keyword *bondlist* correctly treats molecules that span -the box and are bonded to themselves across a periodic boundary, by -relying on self-consistent nearest-image assumptions (rather than -using image flags). The *bondlist* option resets all image flags to -zero. Therefore, the *bondlist* keyword can also be used in general -for systems that may not have consistent image flags. The *bondlist* -algorithm builds off the *bbox* algorithm, so it is fast when using a -large number of processors, but does require temporary use of more -memory. Specifically, each processor must be able to store arrays for -all atoms in the entire system before it is replicated. +All properties of each atom are replicated (except per-atom fix data, +see the Restrictions section below). This includes their velocities, +which may or may not be desirable. New atom IDs are assigned to new +atoms, as are new molecule IDs. Bonds and other topology interactions +are created between pairs of new atoms as well as between old and new +atoms. .. note:: + + The bond discussion which follows only refers to models with + permanent covalent bonds typically defined in LAMMPS via a data + file. It is not relevant to sytems modeled with many-body + potentials which can define bonds on-the-fly, based on the current + positions of nearby atoms, e.g. models using the :doc:`AIREBO + ` or :doc:`ReaxFF ` potentials. - For systems that contain a molecule that spans the box and is - bonded to itself across a periodic boundary (so that the molecule - is effectively a loop), the *bondlist* keyword must be used. A - simple example would be a linear polymer chain that spans the - simulation box and bonds back to itself across the periodic - boundary. More realistic examples would be a CNT (meant to be an - infinitely long CNT) or a graphene sheet or a bulk periodic crystal - where there are explicit bonds specified between near neighbors. - (Note that this restriction only applies to systems that have - permanent bonds as specified in the data file. A CNT that is just - atoms modeled with the :doc:`AIREBO potential ` has no - such permanent bonds, so it can be replicated without the - *bondlist* keyword.) +If the *bond/periodic* keyword is not specified, bond replication is +done by using the image flag for each atom to "unwrap" it out of the +periodic box before replicating it. After replication is performed, +atoms outside the new periodic box are wrapped back into it. This +assigns correct images flags to all atoms in the system. For this to +work, all original atoms in the original simulation box must have +consistent image flags. This means that if two atoms have a bond +between them which crosses a periodic boundary, their respective image +flags will differ by 1 in that dimension. -Restrictions +Image flag consistency is not possible if a system has a periodic bond +loop, meaning there is a chain of bonds which crosses an entire +dimension and re-connects to itself across a periodic boundary. In +this case you MUST use the *bond/periodic* keyword to correctly +replicate the system. This option zeroes the image flags for all +atoms and uses a different algorithm to find new (nearby) bond +neighbors in the replicated system. In the final replicated system +all image flags are zero (in each dimension). + +-- note: + + LAMMPS does not check for image flag consistency before performing + the replication (it does issue a warning about this before a + simulation is run). If the original image flags are inconsistent, + the replicated system will also have inconsistent image flags, but + will otherwise be correctly replicated. This is NOT the case if + there is a periodic bond loop. See the next note. + +-- note: + + LAMMPS does not check for periodic bond loops. If you use the + *bond/periodic* option for a system without periodic bond loops, + the system will be correctly replicated, but image flag information + will be lost (which may or may not be important to your model). If + you do not use the *bond/periodic* option for a system with + periodic bond loops, the replicated system will have invalid bonds + (typically very long), resulting in bad dynamics. + +If possible, the *bbox* keyword should be used when running on a large +number of processors, as it can result in a substantial speed-up for +the replication operation. It uses a bounding box to only check atoms +in replicas that overlap with each processor's new subdomain when +assigning atoms to processors. It also preserves image flag +information. The only drawback to the *bbox* option is that it +requires a temporary use of more memory. Each processor must be able +to store all atoms (and their per-atom data) in the original system, +before it is replicated. + +-- note: + + The algorithm used by the *bond/periodic* keyword builds on the + algorithm used by the *bbox* keyword and thus has the same memory + requirements. If you specify only the *bond/peridoic* keyword it + will internally set the *bbox* keyword as well. + +---------- + + Restrictions """""""""""" A 2d simulation cannot be replicated in the z dimension. If a simulation is non-periodic in a dimension, care should be used -when replicating it in that dimension, as it may put atoms nearly on -top of each other. +when replicating it in that dimension, as it may generate atoms nearly +on top of each other. If the current simulation was read in from a restart file (before a -run is performed), there must not be any fix information stored in -the file for individual atoms. Similarly, no fixes can be defined at -the time the replicate command is used that require vectors of atom +run is performed), there must not be any fix information stored in the +file for individual atoms. Similarly, no fixes can be defined at the +time the replicate command is used that require vectors of atom information to be stored. This is because the replicate command does not know how to replicate that information for new atoms it creates. -To work around this restriction, restart files may be converted into -data files and fixes may be undefined via the :doc:`unfix ` -command before and redefined after the replicate command. + +To work around this restriction two options are possible. (1) Fixes +which use the stored data in the restart file can be defined before +replication and then deleted via the :doc:`unfix ` command and +re-defined after it. Or (2) the restart file can be converted to a +data file (which deletes the stored fix infomation) and fixes defined +after the replicate command. In both these scenarios, the per-atom +fix information in the restart file is lost. Related commands """""""""""""""" none - Default """"""" -none +No settings for using the *bbox* or *bond/periodic* algorithms. diff --git a/examples/README b/examples/README index 86d14e7078..90831b49f0 100644 --- a/examples/README +++ b/examples/README @@ -104,6 +104,7 @@ prd: parallel replica dynamics of vacancy diffusion in bulk Si python: use of PYTHON package to invoke Python code from input script qeq: use of QEQ package for charge equilibration reaxff: RDX and TATB and several other models using ReaxFF +replicate: use of replicate command rerun: use of rerun and read_dump commands rigid: rigid bodies modeled as independent or coupled shear: sideways shear applied to 2d solid, with and without a void diff --git a/examples/replicate/README b/examples/replicate/README new file mode 100644 index 0000000000..1363158b37 --- /dev/null +++ b/examples/replicate/README @@ -0,0 +1,23 @@ +This directory has input scripts which demonstrate how to use the +replicate command both for systems with and without periodic bond +loops. A periodic bond loop is where a chain of bonds spans a +periodic dimension of the box and includes one or more bonds which +cross the periodic boundary to close the loop. + +To run these scripts, LAMMPS should be built with the MOLECULE and +CLASS2 packages. The latter is only needed for the CNT example. + +These scripts are tiny examples which illustrate both kinds of +systems. Each produces a series of images which can be visualized. +If the 3 lines for a dump movie command are uncommented, a MPG movie +is produced, assuming LAMMPS is build with FFMPEG support. + +in.replicate.bond.x # linear chains in x direction, bond loop in x +in.replcate.bond.x.y # 2d grid of bonded atoms, bond loops in x and y +in.replicate.bond.xy # linear chains in diagonal direction, bond loop in x and y +in.replicate.bond.noloop # linear chains in x direction, no bond loop + +This script is for a complex system of 3 orthogonal CNTs which has +periodic bond loops in all 3 dimensions xyz. + +in.replicate.cnt diff --git a/examples/replicate/data.bond.x b/examples/replicate/data.bond.x new file mode 100644 index 0000000000..b5f4d49f2d --- /dev/null +++ b/examples/replicate/data.bond.x @@ -0,0 +1,22 @@ +# system with periodic bonds in x + +3 atoms +3 bonds + +1 atom types +1 bond types + +0 3 xlo xhi +0 1 ylo yhi + +Atoms + +1 1 1 0.5 0.5 0 +2 1 1 1.5 0.5 0 +3 1 1 2.5 0.5 0 + +Bonds + +1 1 1 2 +2 1 2 3 +3 1 3 1 diff --git a/examples/replicate/data.bond.x.noloop b/examples/replicate/data.bond.x.noloop new file mode 100644 index 0000000000..4c096724be --- /dev/null +++ b/examples/replicate/data.bond.x.noloop @@ -0,0 +1,21 @@ +# system with non-periodic bonds in x + +3 atoms +2 bonds + +1 atom types +1 bond types + +0 3 xlo xhi +0 1 ylo yhi + +Atoms + +1 1 1 0.5 0.5 0 0 0 0 +2 1 1 1.5 0.5 0 0 0 0 +3 1 1 2.5 0.5 0 -1 0 0 + +Bonds + +1 1 1 2 +2 1 3 1 diff --git a/examples/replicate/data.bond.x.y b/examples/replicate/data.bond.x.y new file mode 100644 index 0000000000..7eaf19a2ae --- /dev/null +++ b/examples/replicate/data.bond.x.y @@ -0,0 +1,43 @@ +# system with periodic bonds in both x and y + +9 atoms +18 bonds + +1 atom types +1 bond types + +0 3 xlo xhi +0 3 ylo yhi + +Atoms + +1 1 1 0.5 0.5 0 +2 1 1 1.5 0.5 0 +3 1 1 2.5 0.5 0 +4 1 1 0.5 1.5 0 +5 1 1 1.5 1.5 0 +6 1 1 2.5 1.5 0 +7 1 1 0.5 2.5 0 +8 1 1 1.5 2.5 0 +9 1 1 2.5 2.5 0 + +Bonds + +1 1 1 2 +2 1 2 3 +3 1 3 1 +4 1 4 5 +5 1 5 6 +6 1 6 4 +7 1 7 8 +8 1 8 9 +9 1 9 7 +10 1 1 4 +11 1 4 7 +12 1 7 1 +13 1 2 5 +14 1 5 8 +15 1 8 2 +16 1 3 6 +17 1 6 9 +18 1 9 3 diff --git a/examples/replicate/data.bond.xy b/examples/replicate/data.bond.xy new file mode 100644 index 0000000000..31e9d8785a --- /dev/null +++ b/examples/replicate/data.bond.xy @@ -0,0 +1,22 @@ +# system with periodic bonds in xy direction + +3 atoms +3 bonds + +1 atom types +1 bond types + +0 3 xlo xhi +0 3 ylo yhi + +Atoms + +1 1 1 0.5 0.5 0 +2 1 1 1.5 1.5 0 +3 1 1 2.5 2.5 0 + +Bonds + +1 1 1 2 +2 1 2 3 +3 1 3 1 diff --git a/examples/replicate/in.replicate.bond.x b/examples/replicate/in.replicate.bond.x new file mode 100644 index 0000000000..868e05f177 --- /dev/null +++ b/examples/replicate/in.replicate.bond.x @@ -0,0 +1,34 @@ +# test of replicating system with periodic bonds in x + +dimension 2 +atom_style molecular + +read_data data.bond.x + +#replicate 3 3 1 +replicate 3 3 1 bond/periodic + +mass 1 1.0 +velocity all create 0.02 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 + +bond_style harmonic +bond_coeff 1 50.0 1.0 + +special_bonds fene + +fix 1 all nve + +write_data tmp.data.x + +dump 1 all image 100 tmp.image.x.*.ppm type type & + adiam 0.2 bond type 0.1 zoom 1.6 +dump_modify 1 pad 5 + +#dump 2 all movie 100 tmp.movie.x.mpg type type & +# adiam 0.2 bond type 0.1 zoom 1.6 +#dump_modify 2 pad 5 + +run 5000 diff --git a/examples/replicate/in.replicate.bond.x.noloop b/examples/replicate/in.replicate.bond.x.noloop new file mode 100644 index 0000000000..b9862f844d --- /dev/null +++ b/examples/replicate/in.replicate.bond.x.noloop @@ -0,0 +1,34 @@ +# test of replicating system with periodic bonds in x + +dimension 2 +atom_style molecular + +read_data data.bond.x.noloop + +replicate 3 3 1 +#replicate 3 3 1 bond/periodic + +mass 1 1.0 +velocity all create 0.001 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 + +bond_style harmonic +bond_coeff 1 50.0 1.0 + +special_bonds fene + +fix 1 all nve + +write_data tmp.data.x.non + +dump 1 all image 100 tmp.image.x.non.*.ppm type type & + adiam 0.2 bond type 0.1 zoom 1.6 +dump_modify 1 pad 5 + +#dump 2 all movie 100 tmp.movie.x.non.mpg type type & +# adiam 0.2 bond type 0.1 zoom 1.6 +#dump_modify 2 pad 5 + +run 5000 diff --git a/examples/replicate/in.replicate.bond.x.y b/examples/replicate/in.replicate.bond.x.y new file mode 100644 index 0000000000..100350dc18 --- /dev/null +++ b/examples/replicate/in.replicate.bond.x.y @@ -0,0 +1,34 @@ +# test of replicating system with periodic bonds in both x and y + +dimension 2 +atom_style molecular + +read_data data.bond.x.y + +#replicate 3 3 1 +replicate 3 3 1 bond/periodic + +mass 1 1.0 +velocity all create 0.02 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 + +bond_style harmonic +bond_coeff 1 50.0 1.0 + +special_bonds fene + +fix 1 all nve + +write_data tmp.data.x.y + +dump 1 all image 100 tmp.image.x.y.*.ppm type type & + adiam 0.2 bond type 0.1 zoom 1.6 +dump_modify 1 pad 5 + +#dump 2 all movie 100 tmp.movie.x.y.mpg type type & +# adiam 0.2 bond type 0.1 zoom 1.6 +#dump_modify 2 pad 5 + +run 5000 diff --git a/examples/replicate/in.replicate.bond.xy b/examples/replicate/in.replicate.bond.xy new file mode 100644 index 0000000000..52ca79ace7 --- /dev/null +++ b/examples/replicate/in.replicate.bond.xy @@ -0,0 +1,34 @@ +# test of replicating system with periodic bonds in xy diagonal direction + +dimension 2 +atom_style molecular + +read_data data.bond.xy + +#replicate 3 3 1 +replicate 3 3 1 bond/periodic + +mass 1 1.0 +velocity all create 0.02 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.5 + +bond_style harmonic +bond_coeff 1 50.0 1.414 + +special_bonds fene + +fix 1 all nve + +write_data tmp.data.xy + +dump 1 all image 100 tmp.image.xy.*.ppm type type & + adiam 0.2 bond type 0.1 zoom 1.6 +dump_modify 1 pad 5 + +#dump 2 all movie 100 tmp.movie.xy.mpg type type & +# adiam 0.2 bond type 0.1 zoom 1.6 +#dump_modify 2 pad 5 + +run 5000 diff --git a/examples/replicate/in.replicate b/examples/replicate/in.replicate.cnt similarity index 94% rename from examples/replicate/in.replicate rename to examples/replicate/in.replicate.cnt index 52140d4ce8..0b8b384bbb 100644 --- a/examples/replicate/in.replicate +++ b/examples/replicate/in.replicate.cnt @@ -22,7 +22,7 @@ improper_style class2 read_data three_periodic_CNTs.data.gz -replicate 2 2 2 bondlist +replicate 2 2 2 bond/periodic fix 1 all nve diff --git a/examples/replicate/log.6May24.replicate.bond.x.g++.1 b/examples/replicate/log.6May24.replicate.bond.x.g++.1 new file mode 100644 index 0000000000..3f65d11c15 --- /dev/null +++ b/examples/replicate/log.6May24.replicate.bond.x.g++.1 @@ -0,0 +1,125 @@ +LAMMPS (17 Apr 2024) +# test of replicating system with periodic bonds in x + +dimension 2 +atom_style molecular + +read_data data.bond.x +Reading data file ... + orthogonal box = (0 0 -0.5) to (3 1 0.5) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 3 atoms + scanning bonds ... + 1 = max bonds/atom + orthogonal box = (0 0 -0.5) to (3 1 0.5) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 3 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.004 seconds + +#replicate 3 3 1 +replicate 3 3 1 bond/periodic +Replication is creating a 3x3x1 = 9 times larger system... + orthogonal box = (0 0 -0.5) to (9 3 0.5) + 1 by 1 by 1 MPI processor grid + bounding box image = (0 0 0) to (0 0 0) + bounding box extra memory = 0.00 MB + average # of replicas added to proc = 9.00 out of 9 (100.00%) + 27 atoms + 27 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + replicate CPU = 0.001 seconds + +mass 1 1.0 +velocity all create 0.02 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 + +bond_style harmonic +bond_coeff 1 50.0 1.0 + +special_bonds fene +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 2 = max # of 1-2 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +fix 1 all nve + +write_data tmp.data.x +System init for write_data ... +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 7 3 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d + bin: standard + +dump 1 all image 100 tmp.image.x.*.ppm type type adiam 0.2 bond type 0.1 zoom 1.6 +dump_modify 1 pad 5 + +#dump 2 all movie 100 tmp.movie.x.mpg type type # adiam 0.2 bond type 0.1 zoom 1.6 +#dump_modify 2 pad 5 + +run 5000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +WARNING: Inconsistent image flags (../domain.cpp:1051) +Per MPI rank memory allocation (min/avg/max) = 6.302 | 6.302 | 6.302 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0.02 -1.1250229 0 -1.1057636 9.028122 + 5000 0.54111971 -1.9054641 0.29066874 -1.0937172 3.4346743 +Loop time of 0.0764878 on 1 procs for 5000 steps with 27 atoms + +Performance: 28239805.842 tau/day, 65369.921 timesteps/s, 1.765 Matom-step/s +66.5% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0048837 | 0.0048837 | 0.0048837 | 0.0 | 6.38 +Bond | 0.00065879 | 0.00065879 | 0.00065879 | 0.0 | 0.86 +Neigh | 0.0019897 | 0.0019897 | 0.0019897 | 0.0 | 2.60 +Comm | 0.0012815 | 0.0012815 | 0.0012815 | 0.0 | 1.68 +Output | 0.066351 | 0.066351 | 0.066351 | 0.0 | 86.75 +Modify | 0.00069789 | 0.00069789 | 0.00069789 | 0.0 | 0.91 +Other | | 0.0006247 | | | 0.82 + +Nlocal: 27 ave 27 max 27 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 108 ave 108 max 108 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 284 ave 284 max 284 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 284 +Ave neighs/atom = 10.518519 +Ave special neighs/atom = 2 +Neighbor list builds = 287 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/replicate/log.6May24.replicate.bond.x.g++.4 b/examples/replicate/log.6May24.replicate.bond.x.g++.4 new file mode 100644 index 0000000000..9e4423d5f6 --- /dev/null +++ b/examples/replicate/log.6May24.replicate.bond.x.g++.4 @@ -0,0 +1,126 @@ +LAMMPS (17 Apr 2024) +WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551) +# test of replicating system with periodic bonds in x + +dimension 2 +atom_style molecular + +read_data data.bond.x +Reading data file ... + orthogonal box = (0 0 -0.5) to (3 1 0.5) + 4 by 1 by 1 MPI processor grid + reading atoms ... + 3 atoms + scanning bonds ... + 1 = max bonds/atom + orthogonal box = (0 0 -0.5) to (3 1 0.5) + 4 by 1 by 1 MPI processor grid + reading bonds ... + 3 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.003 seconds + +#replicate 3 3 1 +replicate 3 3 1 bond/periodic +Replication is creating a 3x3x1 = 9 times larger system... + orthogonal box = (0 0 -0.5) to (9 3 0.5) + 4 by 1 by 1 MPI processor grid + bounding box image = (0 0 0) to (0 0 0) + bounding box extra memory = 0.00 MB + average # of replicas added to proc = 5.25 out of 9 (58.33%) + 27 atoms + 27 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + replicate CPU = 0.002 seconds + +mass 1 1.0 +velocity all create 0.02 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 + +bond_style harmonic +bond_coeff 1 50.0 1.0 + +special_bonds fene +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 2 = max # of 1-2 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +fix 1 all nve + +write_data tmp.data.x +System init for write_data ... +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 7 3 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d + bin: standard + +dump 1 all image 100 tmp.image.x.*.ppm type type adiam 0.2 bond type 0.1 zoom 1.6 +dump_modify 1 pad 5 + +#dump 2 all movie 100 tmp.movie.x.mpg type type # adiam 0.2 bond type 0.1 zoom 1.6 +#dump_modify 2 pad 5 + +run 5000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +WARNING: Inconsistent image flags (../domain.cpp:1051) +Per MPI rank memory allocation (min/avg/max) = 6.309 | 6.309 | 6.309 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0.02 -1.1250229 0 -1.1057636 9.028122 + 5000 0.50911963 -1.7968226 0.21209852 -1.0944607 4.1676488 +Loop time of 0.21682 on 4 procs for 5000 steps with 27 atoms + +Performance: 9962160.612 tau/day, 23060.557 timesteps/s, 622.635 katom-step/s +93.9% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.001787 | 0.0021247 | 0.0028772 | 1.0 | 0.98 +Bond | 0.00039682 | 0.00045617 | 0.00059887 | 0.0 | 0.21 +Neigh | 0.0013626 | 0.0014006 | 0.0014798 | 0.1 | 0.65 +Comm | 0.017009 | 0.01791 | 0.018656 | 0.5 | 8.26 +Output | 0.06892 | 0.12188 | 0.18918 | 13.7 | 56.21 +Modify | 0.00060336 | 0.00072159 | 0.00088047 | 0.0 | 0.33 +Other | | 0.07233 | | | 33.36 + +Nlocal: 6.75 ave 7 max 6 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Nghost: 64.5 ave 65 max 63 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Neighs: 70.25 ave 77 max 60 min +Histogram: 1 0 0 0 0 1 0 0 1 1 + +Total # of neighbors = 281 +Ave neighs/atom = 10.407407 +Ave special neighs/atom = 2 +Neighbor list builds = 287 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/replicate/log.6May24.replicate.bond.x.noloop.g++.1 b/examples/replicate/log.6May24.replicate.bond.x.noloop.g++.1 new file mode 100644 index 0000000000..54893b449a --- /dev/null +++ b/examples/replicate/log.6May24.replicate.bond.x.noloop.g++.1 @@ -0,0 +1,121 @@ +LAMMPS (17 Apr 2024) +# test of replicating system with periodic bonds in x + +dimension 2 +atom_style molecular + +read_data data.bond.x.non +Reading data file ... + orthogonal box = (0 0 -0.5) to (3 1 0.5) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 3 atoms + scanning bonds ... + 1 = max bonds/atom + orthogonal box = (0 0 -0.5) to (3 1 0.5) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.004 seconds + +replicate 3 3 1 +Replication is creating a 3x3x1 = 9 times larger system... + orthogonal box = (0 0 -0.5) to (9 3 0.5) + 1 by 1 by 1 MPI processor grid + 27 atoms + 18 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + replicate CPU = 0.001 seconds +#replicate 3 3 1 bond/periodic + +mass 1 1.0 +velocity all create 0.001 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 + +bond_style harmonic +bond_coeff 1 50.0 1.0 + +special_bonds fene +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + +fix 1 all nve + +write_data tmp.data.x.non +System init for write_data ... +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 7 3 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d + bin: standard + +dump 1 all image 100 tmp.image.x.non.*.ppm type type adiam 0.2 bond type 0.1 zoom 1.6 +dump_modify 1 pad 5 + +#dump 2 all movie 100 tmp.movie.x.non.mpg type type # adiam 0.2 bond type 0.1 zoom 1.6 +#dump_modify 2 pad 5 + +run 5000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 6.052 | 6.052 | 6.052 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0.001 -1.1250229 0 -1.1240599 13.009826 + 5000 0.62003692 -2.0147214 0.30861545 -1.1090334 8.0279226 +Loop time of 0.0734456 on 1 procs for 5000 steps with 27 atoms + +Performance: 29409520.548 tau/day, 68077.594 timesteps/s, 1.838 Matom-step/s +94.4% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0051444 | 0.0051444 | 0.0051444 | 0.0 | 7.00 +Bond | 0.00048789 | 0.00048789 | 0.00048789 | 0.0 | 0.66 +Neigh | 0.0019333 | 0.0019333 | 0.0019333 | 0.0 | 2.63 +Comm | 0.001332 | 0.001332 | 0.001332 | 0.0 | 1.81 +Output | 0.063139 | 0.063139 | 0.063139 | 0.0 | 85.97 +Modify | 0.00077014 | 0.00077014 | 0.00077014 | 0.0 | 1.05 +Other | | 0.0006387 | | | 0.87 + +Nlocal: 27 ave 27 max 27 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 101 ave 101 max 101 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 288 ave 288 max 288 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 288 +Ave neighs/atom = 10.666667 +Ave special neighs/atom = 1.3333333 +Neighbor list builds = 322 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/replicate/log.6May24.replicate.bond.x.noloop.g++.4 b/examples/replicate/log.6May24.replicate.bond.x.noloop.g++.4 new file mode 100644 index 0000000000..54d9741781 --- /dev/null +++ b/examples/replicate/log.6May24.replicate.bond.x.noloop.g++.4 @@ -0,0 +1,122 @@ +LAMMPS (17 Apr 2024) +WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551) +# test of replicating system with periodic bonds in x + +dimension 2 +atom_style molecular + +read_data data.bond.x.non +Reading data file ... + orthogonal box = (0 0 -0.5) to (3 1 0.5) + 4 by 1 by 1 MPI processor grid + reading atoms ... + 3 atoms + scanning bonds ... + 1 = max bonds/atom + orthogonal box = (0 0 -0.5) to (3 1 0.5) + 4 by 1 by 1 MPI processor grid + reading bonds ... + 2 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.004 seconds + +replicate 3 3 1 +Replication is creating a 3x3x1 = 9 times larger system... + orthogonal box = (0 0 -0.5) to (9 3 0.5) + 4 by 1 by 1 MPI processor grid + 27 atoms + 18 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + replicate CPU = 0.002 seconds +#replicate 3 3 1 bond/periodic + +mass 1 1.0 +velocity all create 0.001 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 + +bond_style harmonic +bond_coeff 1 50.0 1.0 + +special_bonds fene +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + +fix 1 all nve + +write_data tmp.data.x.non +System init for write_data ... +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 7 3 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d + bin: standard + +dump 1 all image 100 tmp.image.x.non.*.ppm type type adiam 0.2 bond type 0.1 zoom 1.6 +dump_modify 1 pad 5 + +#dump 2 all movie 100 tmp.movie.x.non.mpg type type # adiam 0.2 bond type 0.1 zoom 1.6 +#dump_modify 2 pad 5 + +run 5000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Per MPI rank memory allocation (min/avg/max) = 6.059 | 6.059 | 6.059 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0.001 -1.1250229 0 -1.1240599 13.009826 + 5000 0.74931971 -2.233724 0.40158766 -1.1105692 5.6354701 +Loop time of 0.197835 on 4 procs for 5000 steps with 27 atoms + +Performance: 10918214.594 tau/day, 25273.645 timesteps/s, 682.388 katom-step/s +88.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0018771 | 0.0021131 | 0.0027188 | 0.8 | 1.07 +Bond | 0.00032659 | 0.00038248 | 0.00049555 | 0.0 | 0.19 +Neigh | 0.001385 | 0.0014211 | 0.0014704 | 0.1 | 0.72 +Comm | 0.017163 | 0.017405 | 0.017805 | 0.2 | 8.80 +Output | 0.070971 | 0.11052 | 0.17112 | 12.1 | 55.87 +Modify | 0.00058993 | 0.00067708 | 0.00075608 | 0.0 | 0.34 +Other | | 0.06532 | | | 33.02 + +Nlocal: 6.75 ave 7 max 6 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Nghost: 59.75 ave 60 max 59 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Neighs: 72 ave 79 max 63 min +Histogram: 1 0 0 0 0 0 2 0 0 1 + +Total # of neighbors = 288 +Ave neighs/atom = 10.666667 +Ave special neighs/atom = 1.3333333 +Neighbor list builds = 323 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/replicate/log.6May24.replicate.bond.x.y.g++.1 b/examples/replicate/log.6May24.replicate.bond.x.y.g++.1 new file mode 100644 index 0000000000..45308d9a90 --- /dev/null +++ b/examples/replicate/log.6May24.replicate.bond.x.y.g++.1 @@ -0,0 +1,125 @@ +LAMMPS (17 Apr 2024) +# test of replicating system with periodic bonds in both x and y + +dimension 2 +atom_style molecular + +read_data data.bond.x.y +Reading data file ... + orthogonal box = (0 0 -0.5) to (3 3 0.5) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 9 atoms + scanning bonds ... + 2 = max bonds/atom + orthogonal box = (0 0 -0.5) to (3 3 0.5) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 18 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 12 = max # of 1-3 neighbors + 48 = max # of 1-4 neighbors + 8 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.004 seconds + +#replicate 3 3 1 +replicate 3 3 1 bond/periodic +Replication is creating a 3x3x1 = 9 times larger system... + orthogonal box = (0 0 -0.5) to (9 9 0.5) + 1 by 1 by 1 MPI processor grid + bounding box image = (0 0 0) to (0 0 0) + bounding box extra memory = 0.00 MB + average # of replicas added to proc = 9.00 out of 9 (100.00%) + 81 atoms + 162 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 12 = max # of 1-3 neighbors + 48 = max # of 1-4 neighbors + 24 = max # of special neighbors + special bonds CPU = 0.000 seconds + replicate CPU = 0.001 seconds + +mass 1 1.0 +velocity all create 0.02 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 + +bond_style harmonic +bond_coeff 1 50.0 1.0 + +special_bonds fene +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 4 = max # of 1-2 neighbors + 24 = max # of special neighbors + special bonds CPU = 0.000 seconds + +fix 1 all nve + +write_data tmp.data.x.y +System init for write_data ... +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 7 7 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d + bin: standard + +dump 1 all image 100 tmp.image.x.y.*.ppm type type adiam 0.2 bond type 0.1 zoom 1.6 +dump_modify 1 pad 5 + +#dump 2 all movie 100 tmp.movie.x.y.mpg type type # adiam 0.2 bond type 0.1 zoom 1.6 +#dump_modify 2 pad 5 + +run 5000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +WARNING: Inconsistent image flags (../domain.cpp:1051) +Per MPI rank memory allocation (min/avg/max) = 7.555 | 7.555 | 7.555 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0.02 -1.1250229 0 -1.1052698 -2.9713842 + 5000 0.046175679 -1.2280388 0.080003864 -1.1024293 -4.1097897 +Loop time of 0.212344 on 1 procs for 5000 steps with 81 atoms + +Performance: 10172161.526 tau/day, 23546.670 timesteps/s, 1.907 Matom-step/s +93.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.01283 | 0.01283 | 0.01283 | 0.0 | 6.04 +Bond | 0.0032785 | 0.0032785 | 0.0032785 | 0.0 | 1.54 +Neigh | 0.0018379 | 0.0018379 | 0.0018379 | 0.0 | 0.87 +Comm | 0.0016247 | 0.0016247 | 0.0016247 | 0.0 | 0.77 +Output | 0.18991 | 0.18991 | 0.18991 | 0.0 | 89.44 +Modify | 0.0018198 | 0.0018198 | 0.0018198 | 0.0 | 0.86 +Other | | 0.001039 | | | 0.49 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 144 ave 144 max 144 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 714 ave 714 max 714 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 714 +Ave neighs/atom = 8.8148148 +Ave special neighs/atom = 4 +Neighbor list builds = 72 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/replicate/log.6May24.replicate.bond.x.y.g++.4 b/examples/replicate/log.6May24.replicate.bond.x.y.g++.4 new file mode 100644 index 0000000000..f232a4e428 --- /dev/null +++ b/examples/replicate/log.6May24.replicate.bond.x.y.g++.4 @@ -0,0 +1,126 @@ +LAMMPS (17 Apr 2024) +WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551) +# test of replicating system with periodic bonds in both x and y + +dimension 2 +atom_style molecular + +read_data data.bond.x.y +Reading data file ... + orthogonal box = (0 0 -0.5) to (3 3 0.5) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 9 atoms + scanning bonds ... + 2 = max bonds/atom + orthogonal box = (0 0 -0.5) to (3 3 0.5) + 2 by 2 by 1 MPI processor grid + reading bonds ... + 18 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 12 = max # of 1-3 neighbors + 48 = max # of 1-4 neighbors + 8 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.003 seconds + +#replicate 3 3 1 +replicate 3 3 1 bond/periodic +Replication is creating a 3x3x1 = 9 times larger system... + orthogonal box = (0 0 -0.5) to (9 9 0.5) + 2 by 2 by 1 MPI processor grid + bounding box image = (0 0 0) to (0 0 0) + bounding box extra memory = 0.00 MB + average # of replicas added to proc = 6.25 out of 9 (69.44%) + 81 atoms + 162 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 12 = max # of 1-3 neighbors + 48 = max # of 1-4 neighbors + 24 = max # of special neighbors + special bonds CPU = 0.000 seconds + replicate CPU = 0.001 seconds + +mass 1 1.0 +velocity all create 0.02 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 + +bond_style harmonic +bond_coeff 1 50.0 1.0 + +special_bonds fene +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 4 = max # of 1-2 neighbors + 24 = max # of special neighbors + special bonds CPU = 0.000 seconds + +fix 1 all nve + +write_data tmp.data.x.y +System init for write_data ... +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 7 7 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d + bin: standard + +dump 1 all image 100 tmp.image.x.y.*.ppm type type adiam 0.2 bond type 0.1 zoom 1.6 +dump_modify 1 pad 5 + +#dump 2 all movie 100 tmp.movie.x.y.mpg type type # adiam 0.2 bond type 0.1 zoom 1.6 +#dump_modify 2 pad 5 + +run 5000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +WARNING: Inconsistent image flags (../domain.cpp:1051) +Per MPI rank memory allocation (min/avg/max) = 7.552 | 7.552 | 7.552 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0.02 -1.1250229 0 -1.1052698 -2.9713842 + 5000 0.046175679 -1.2280388 0.080003864 -1.1024293 -4.1097897 +Loop time of 0.273847 on 4 procs for 5000 steps with 81 atoms + +Performance: 7887622.810 tau/day, 18258.386 timesteps/s, 1.479 Matom-step/s +92.4% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0039465 | 0.0042593 | 0.0046129 | 0.4 | 1.56 +Bond | 0.0011489 | 0.001207 | 0.0012757 | 0.2 | 0.44 +Neigh | 0.00079819 | 0.0008044 | 0.00081324 | 0.0 | 0.29 +Comm | 0.024107 | 0.024703 | 0.025269 | 0.3 | 9.02 +Output | 0.14406 | 0.18123 | 0.23779 | 8.7 | 66.18 +Modify | 0.00089401 | 0.00095321 | 0.0010422 | 0.0 | 0.35 +Other | | 0.06069 | | | 22.16 + +Nlocal: 20.25 ave 22 max 19 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Nghost: 81.5 ave 82 max 80 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Neighs: 178.5 ave 195 max 165 min +Histogram: 2 0 0 0 0 0 0 1 0 1 + +Total # of neighbors = 714 +Ave neighs/atom = 8.8148148 +Ave special neighs/atom = 4 +Neighbor list builds = 72 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/replicate/log.6May24.replicate.bond.xy.g++.1 b/examples/replicate/log.6May24.replicate.bond.xy.g++.1 new file mode 100644 index 0000000000..207b65ef9b --- /dev/null +++ b/examples/replicate/log.6May24.replicate.bond.xy.g++.1 @@ -0,0 +1,125 @@ +LAMMPS (17 Apr 2024) +# test of replicating system with periodic bonds in xy diagonal direction + +dimension 2 +atom_style molecular + +read_data data.bond.xy +Reading data file ... + orthogonal box = (0 0 -0.5) to (3 3 0.5) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 3 atoms + scanning bonds ... + 1 = max bonds/atom + orthogonal box = (0 0 -0.5) to (3 3 0.5) + 1 by 1 by 1 MPI processor grid + reading bonds ... + 3 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.004 seconds + +#replicate 3 3 1 +replicate 3 3 1 bond/periodic +Replication is creating a 3x3x1 = 9 times larger system... + orthogonal box = (0 0 -0.5) to (9 9 0.5) + 1 by 1 by 1 MPI processor grid + bounding box image = (0 0 0) to (0 0 0) + bounding box extra memory = 0.00 MB + average # of replicas added to proc = 9.00 out of 9 (100.00%) + 27 atoms + 27 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + replicate CPU = 0.001 seconds + +mass 1 1.0 +velocity all create 0.02 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.5 + +bond_style harmonic +bond_coeff 1 50.0 1.414 + +special_bonds fene +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 2 = max # of 1-2 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +fix 1 all nve + +write_data tmp.data.xy +System init for write_data ... +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 7 7 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d + bin: standard + +dump 1 all image 100 tmp.image.xy.*.ppm type type adiam 0.2 bond type 0.1 zoom 1.6 +dump_modify 1 pad 5 + +#dump 2 all movie 100 tmp.movie.xy.mpg type type # adiam 0.2 bond type 0.1 zoom 1.6 +#dump_modify 2 pad 5 + +run 5000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +WARNING: Inconsistent image flags (../domain.cpp:1051) +Per MPI rank memory allocation (min/avg/max) = 6.302 | 6.302 | 6.302 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0.02 -0.66256987 2.2804444e-06 -0.64330834 -0.59475371 + 5000 0.43110862 -1.1484506 0.16888799 -0.56442095 -0.3683968 +Loop time of 0.124095 on 1 procs for 5000 steps with 27 atoms + +Performance: 17406010.885 tau/day, 40291.692 timesteps/s, 1.088 Matom-step/s +82.3% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0013734 | 0.0013734 | 0.0013734 | 0.0 | 1.11 +Bond | 0.00064058 | 0.00064058 | 0.00064058 | 0.0 | 0.52 +Neigh | 0.00090424 | 0.00090424 | 0.00090424 | 0.0 | 0.73 +Comm | 0.00081732 | 0.00081732 | 0.00081732 | 0.0 | 0.66 +Output | 0.11905 | 0.11905 | 0.11905 | 0.0 | 95.93 +Modify | 0.0007252 | 0.0007252 | 0.0007252 | 0.0 | 0.58 +Other | | 0.0005888 | | | 0.47 + +Nlocal: 27 ave 27 max 27 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 45 ave 45 max 45 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 66 ave 66 max 66 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 66 +Ave neighs/atom = 2.4444444 +Ave special neighs/atom = 2 +Neighbor list builds = 244 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/replicate/log.6May24.replicate.bond.xy.g++.4 b/examples/replicate/log.6May24.replicate.bond.xy.g++.4 new file mode 100644 index 0000000000..a8ef944ec7 --- /dev/null +++ b/examples/replicate/log.6May24.replicate.bond.xy.g++.4 @@ -0,0 +1,126 @@ +LAMMPS (17 Apr 2024) +WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551) +# test of replicating system with periodic bonds in xy diagonal direction + +dimension 2 +atom_style molecular + +read_data data.bond.xy +Reading data file ... + orthogonal box = (0 0 -0.5) to (3 3 0.5) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 3 atoms + scanning bonds ... + 1 = max bonds/atom + orthogonal box = (0 0 -0.5) to (3 3 0.5) + 2 by 2 by 1 MPI processor grid + reading bonds ... + 3 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 2 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.003 seconds + +#replicate 3 3 1 +replicate 3 3 1 bond/periodic +Replication is creating a 3x3x1 = 9 times larger system... + orthogonal box = (0 0 -0.5) to (9 9 0.5) + 2 by 2 by 1 MPI processor grid + bounding box image = (0 0 0) to (0 0 0) + bounding box extra memory = 0.00 MB + average # of replicas added to proc = 6.25 out of 9 (69.44%) + 27 atoms + 27 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + replicate CPU = 0.001 seconds + +mass 1 1.0 +velocity all create 0.02 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.5 + +bond_style harmonic +bond_coeff 1 50.0 1.414 + +special_bonds fene +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 1 1 + special bond factors coul: 0 1 1 + 2 = max # of 1-2 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + +fix 1 all nve + +write_data tmp.data.xy +System init for write_data ... +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 7 7 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d + bin: standard + +dump 1 all image 100 tmp.image.xy.*.ppm type type adiam 0.2 bond type 0.1 zoom 1.6 +dump_modify 1 pad 5 + +#dump 2 all movie 100 tmp.movie.xy.mpg type type # adiam 0.2 bond type 0.1 zoom 1.6 +#dump_modify 2 pad 5 + +run 5000 +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +WARNING: Inconsistent image flags (../domain.cpp:1051) +Per MPI rank memory allocation (min/avg/max) = 6.301 | 6.301 | 6.301 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0.02 -0.66256988 2.2804444e-06 -0.64330834 -0.59475371 + 5000 0.43110877 -1.1484507 0.168888 -0.56442093 -0.36839692 +Loop time of 0.286423 on 4 procs for 5000 steps with 27 atoms + +Performance: 7541285.935 tau/day, 17456.680 timesteps/s, 471.330 katom-step/s +92.9% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00054941 | 0.00084836 | 0.0013689 | 0.0 | 0.30 +Bond | 0.00034068 | 0.00045816 | 0.00068461 | 0.0 | 0.16 +Neigh | 0.00092076 | 0.00098494 | 0.0010463 | 0.0 | 0.34 +Comm | 0.018151 | 0.018737 | 0.019531 | 0.4 | 6.54 +Output | 0.13261 | 0.19363 | 0.2596 | 10.7 | 67.60 +Modify | 0.00053153 | 0.00071381 | 0.0010268 | 0.0 | 0.25 +Other | | 0.07105 | | | 24.81 + +Nlocal: 6.75 ave 9 max 5 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 26.25 ave 28 max 25 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Neighs: 16.5 ave 23 max 10 min +Histogram: 1 1 0 0 0 0 0 0 1 1 + +Total # of neighbors = 66 +Ave neighs/atom = 2.4444444 +Ave special neighs/atom = 2 +Neighbor list builds = 244 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/replicate/log.7Jan22.replicate.g++.1 b/examples/replicate/log.6May24.replicate.cnt.g++.1 similarity index 67% rename from examples/replicate/log.7Jan22.replicate.g++.1 rename to examples/replicate/log.6May24.replicate.cnt.g++.1 index 2933535ae8..f44032e723 100644 --- a/examples/replicate/log.7Jan22.replicate.g++.1 +++ b/examples/replicate/log.6May24.replicate.cnt.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (7 Jan 2022) +LAMMPS (17 Apr 2024) # three orthogonal periodic CNTs # demo for replicating triply looped system # infinite loops in x, y, z @@ -37,6 +37,8 @@ Reading data file ... 12 = max dihedrals/atom scanning impropers ... 1 = max impropers/atom + orthogonal box = (0 0 0) to (80.96 80.96 80.96) + 1 by 1 by 1 MPI processor grid reading bonds ... 4752 bonds reading angles ... @@ -52,11 +54,11 @@ Finding 1-2 1-3 1-4 neighbors ... 6 = max # of 1-3 neighbors 18 = max # of 1-4 neighbors 18 = max # of special neighbors - special bonds CPU = 0.003 seconds - read_data CPU = 0.115 seconds + special bonds CPU = 0.002 seconds + read_data CPU = 0.056 seconds -replicate 2 2 2 bondlist -Replicating atoms ... +replicate 2 2 2 bond/periodic +Replication is creating a 2x2x2 = 8 times larger system... orthogonal box = (0 0 0) to (161.92 161.92 161.92) 1 by 1 by 1 MPI processor grid bounding box image = (0 0 0) to (0 0 0) @@ -74,15 +76,15 @@ Finding 1-2 1-3 1-4 neighbors ... 6 = max # of 1-3 neighbors 18 = max # of 1-4 neighbors 18 = max # of special neighbors - special bonds CPU = 0.021 seconds - replicate CPU = 0.052 seconds + special bonds CPU = 0.012 seconds + replicate CPU = 0.027 seconds fix 1 all nve run 100 - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Generated 0 of 0 mixed pair_coeff terms from sixthpower/geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 @@ -93,26 +95,26 @@ Neighbor list info ... pair build: half/bin/newton stencil: half/bin/3d bin: standard -WARNING: Inconsistent image flags (../domain.cpp:814) +WARNING: Inconsistent image flags (../domain.cpp:1051) Per MPI rank memory allocation (min/avg/max) = 51.87 | 51.87 | 51.87 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -14266.189 1466925.5 1452659.3 -29908.753 - 100 2155.9128 -17224.188 1306769.8 1452409 1985.2082 -Loop time of 15.0972 on 1 procs for 100 steps with 25344 atoms + Step Temp E_pair E_mol TotEng Press + 0 0 -14266.189 1466925.5 1452659.3 -29908.753 + 100 2155.9128 -17224.188 1306769.8 1452409 1985.2082 +Loop time of 5.0155 on 1 procs for 100 steps with 25344 atoms -Performance: 0.572 ns/day, 41.937 hours/ns, 6.624 timesteps/s +Performance: 1.723 ns/day, 13.932 hours/ns, 19.938 timesteps/s, 505.314 katom-step/s 100.0% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 3.7175 | 3.7175 | 3.7175 | 0.0 | 24.62 -Bond | 11.222 | 11.222 | 11.222 | 0.0 | 74.33 -Neigh | 0.1032 | 0.1032 | 0.1032 | 0.0 | 0.68 -Comm | 0.014487 | 0.014487 | 0.014487 | 0.0 | 0.10 -Output | 0.00010894 | 0.00010894 | 0.00010894 | 0.0 | 0.00 -Modify | 0.027112 | 0.027112 | 0.027112 | 0.0 | 0.18 -Other | | 0.01274 | | | 0.08 +Pair | 1.6557 | 1.6557 | 1.6557 | 0.0 | 33.01 +Bond | 3.2813 | 3.2813 | 3.2813 | 0.0 | 65.42 +Neigh | 0.047025 | 0.047025 | 0.047025 | 0.0 | 0.94 +Comm | 0.0085317 | 0.0085317 | 0.0085317 | 0.0 | 0.17 +Output | 7.8551e-05 | 7.8551e-05 | 7.8551e-05 | 0.0 | 0.00 +Modify | 0.014635 | 0.014635 | 0.014635 | 0.0 | 0.29 +Other | | 0.008159 | | | 0.16 Nlocal: 25344 ave 25344 max 25344 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -129,4 +131,4 @@ Dangerous builds = 0 # write_restart replicate.restart # write_data replicate.data -Total wall time: 0:00:15 +Total wall time: 0:00:05 diff --git a/examples/replicate/log.7Jan22.replicate.g++.4 b/examples/replicate/log.6May24.replicate.cnt.g++.4 similarity index 65% rename from examples/replicate/log.7Jan22.replicate.g++.4 rename to examples/replicate/log.6May24.replicate.cnt.g++.4 index 79a13b1484..57abdf767d 100644 --- a/examples/replicate/log.7Jan22.replicate.g++.4 +++ b/examples/replicate/log.6May24.replicate.cnt.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (7 Jan 2022) +LAMMPS (17 Apr 2024) +WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (../lammps.cpp:551) # three orthogonal periodic CNTs # demo for replicating triply looped system # infinite loops in x, y, z @@ -37,6 +38,8 @@ Reading data file ... 12 = max dihedrals/atom scanning impropers ... 1 = max impropers/atom + orthogonal box = (0 0 0) to (80.96 80.96 80.96) + 1 by 2 by 2 MPI processor grid reading bonds ... 4752 bonds reading angles ... @@ -53,10 +56,10 @@ Finding 1-2 1-3 1-4 neighbors ... 18 = max # of 1-4 neighbors 18 = max # of special neighbors special bonds CPU = 0.001 seconds - read_data CPU = 0.315 seconds + read_data CPU = 0.064 seconds -replicate 2 2 2 bondlist -Replicating atoms ... +replicate 2 2 2 bond/periodic +Replication is creating a 2x2x2 = 8 times larger system... orthogonal box = (0 0 0) to (161.92 161.92 161.92) 1 by 2 by 2 MPI processor grid bounding box image = (0 0 0) to (0 0 0) @@ -74,15 +77,15 @@ Finding 1-2 1-3 1-4 neighbors ... 6 = max # of 1-3 neighbors 18 = max # of 1-4 neighbors 18 = max # of special neighbors - special bonds CPU = 0.007 seconds - replicate CPU = 0.020 seconds + special bonds CPU = 0.004 seconds + replicate CPU = 0.012 seconds fix 1 all nve run 100 - generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Generated 0 of 0 mixed pair_coeff terms from sixthpower/geometric mixing rule Neighbor list info ... - update every 1 steps, delay 10 steps, check yes + update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 @@ -93,26 +96,26 @@ Neighbor list info ... pair build: half/bin/newton stencil: half/bin/3d bin: standard -WARNING: Inconsistent image flags (../domain.cpp:814) +WARNING: Inconsistent image flags (../domain.cpp:1051) Per MPI rank memory allocation (min/avg/max) = 28.69 | 28.69 | 28.69 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -14266.189 1466925.5 1452659.3 -29908.753 - 100 2155.9128 -17224.188 1306769.8 1452409 1985.2082 -Loop time of 4.13195 on 4 procs for 100 steps with 25344 atoms + Step Temp E_pair E_mol TotEng Press + 0 0 -14266.189 1466925.5 1452659.3 -29908.753 + 100 2155.9128 -17224.188 1306769.8 1452409 1985.2082 +Loop time of 1.3667 on 4 procs for 100 steps with 25344 atoms -Performance: 2.091 ns/day, 11.478 hours/ns, 24.202 timesteps/s -100.0% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 6.322 ns/day, 3.796 hours/ns, 73.169 timesteps/s, 1.854 Matom-step/s +99.8% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.99372 | 1.014 | 1.0672 | 3.1 | 24.54 -Bond | 2.9449 | 2.9795 | 3.0136 | 2.0 | 72.11 -Neigh | 0.026695 | 0.026706 | 0.026716 | 0.0 | 0.65 -Comm | 0.012404 | 0.099546 | 0.15425 | 18.7 | 2.41 -Output | 4.3822e-05 | 5.0693e-05 | 7.0516e-05 | 0.0 | 0.00 -Modify | 0.0074219 | 0.0074887 | 0.0075411 | 0.1 | 0.18 -Other | | 0.004616 | | | 0.11 +Pair | 0.43424 | 0.43539 | 0.43741 | 0.2 | 31.86 +Bond | 0.88613 | 0.89013 | 0.90094 | 0.7 | 65.13 +Neigh | 0.013198 | 0.013199 | 0.013201 | 0.0 | 0.97 +Comm | 0.010742 | 0.020522 | 0.02546 | 4.1 | 1.50 +Output | 3.2788e-05 | 3.6302e-05 | 4.4556e-05 | 0.0 | 0.00 +Modify | 0.0042029 | 0.0042366 | 0.004267 | 0.0 | 0.31 +Other | | 0.003188 | | | 0.23 Nlocal: 6336 ave 6336 max 6336 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -129,4 +132,4 @@ Dangerous builds = 0 # write_restart replicate.restart # write_data replicate.data -Total wall time: 0:00:04 +Total wall time: 0:00:01 diff --git a/src/replicate.cpp b/src/replicate.cpp index ca432b32a8..e232160842 100644 --- a/src/replicate.cpp +++ b/src/replicate.cpp @@ -12,6 +12,12 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + Contributing authors: + Chris Knight (ANL) for bbox option + Jake Gissinger (Stevens Institute of Technology) for bond/periodic option +------------------------------------------------------------------------- */ + #include "replicate.h" #include "accelerator_kokkos.h" @@ -70,13 +76,24 @@ void Replicate::command(int narg, char **arg) utils::logmesg(lmp, "Replication is creating a {}x{}x{} = {} times larger system...\n", nx, ny, nz, nrep); - int bbox_flag = 0; - int bondlist_flag = 0; - if (narg == 4) { - if (strcmp(arg[3],"bbox") == 0) bbox_flag = 1; - if (strcmp(arg[3],"bondlist") == 0) bondlist_flag = 1; + // optional keywords + + bbox_flag = 0; + bond_flag = 0; + + int iarg = 3; + while (iarg < narg) { + if (strcmp(arg[iarg],"bbox") == 0) { + bbox_flag = 1; + iarg++; + } else if (strcmp(arg[iarg],"bond/periodic") == 0) { + bond_flag = 1; + iarg++; + } else error->all(FLERR,"Illegal replicate command"); } + if (bond_flag) bbox_flag = 1; + // error and warning checks if (nx <= 0 || ny <= 0 || nz <= 0) @@ -91,7 +108,7 @@ void Replicate::command(int narg, char **arg) } if (atom->nextra_grow || atom->nextra_restart || atom->nextra_store) - error->all(FLERR,"Cannot replicate with fixes that store atom quantities"); + error->all(FLERR,"Cannot replicate with fixes that store per-atom quantities"); // record wall time for atom replication @@ -110,24 +127,24 @@ void Replicate::command(int narg, char **arg) // maxmol = largest molecule tag across all existing atoms - tagint maxmol = 0; + maxmol = 0; if (atom->molecule_flag) { for (i = 0; i < atom->nlocal; i++) maxmol = MAX(atom->molecule[i],maxmol); tagint maxmol_all; MPI_Allreduce(&maxmol,&maxmol_all,1,MPI_LMP_TAGINT,MPI_MAX,world); maxmol = maxmol_all; } - - // reset image flags for bondlist option - if (bondlist_flag) + + // reset image flags to zero for bond/periodic option + + if (bond_flag) for (i=0; inlocal; ++i) atom->image[i] = ((imageint) IMGMAX << IMG2BITS) | ((imageint) IMGMAX << IMGBITS) | IMGMAX; - // check image flags maximum extent + // _imagelo/hi = maximum extent of image flags in each dimension // only efficient small image flags compared to new system - int _imagelo[3], _imagehi[3]; _imagelo[0] = 0; _imagelo[1] = 0; _imagelo[2] = 0; @@ -135,7 +152,7 @@ void Replicate::command(int narg, char **arg) _imagehi[1] = 0; _imagehi[2] = 0; - if (bbox_flag || bondlist_flag) { + if (bbox_flag || bond_flag) { for (i=0; inlocal; ++i) { imageint image = atom->image[i]; @@ -157,14 +174,14 @@ void Replicate::command(int narg, char **arg) } // unmap existing atoms via image flags + // no-op for bond/periodic option for (i = 0; i < atom->nlocal; i++) domain->unmap(atom->x[i],atom->image[i]); - + // communication buffer for all my atom's info // max_size = largest buffer needed by any proc - // must do before new Atom class created, - // since size_restart() uses atom->nlocal + // must do before new Atom class created, since size_restart() uses atom->nlocal int max_size; int send_size = atom->avec->size_restart(); @@ -177,7 +194,7 @@ void Replicate::command(int narg, char **arg) // atom = new replicated atom class // also set atomKK for Kokkos version of Atom class - Atom *old = atom; + old = atom; atomKK = nullptr; if (lmp->kokkos) atom = atomKK = new AtomKokkos(lmp); else atom = new Atom(lmp); @@ -216,7 +233,7 @@ void Replicate::command(int narg, char **arg) nrep*old->nimpropers < 0 || nrep*old->nimpropers >= MAXBIGINT) error->all(FLERR,"Replicated system is too big"); - // assign atom and topology counts in new class from old one + // assign atom and topology counts in new Atom class from old Atom class atom->natoms = old->natoms * nrep; atom->nbonds = old->nbonds * nrep; @@ -258,18 +275,18 @@ void Replicate::command(int narg, char **arg) // store old simulation box int triclinic = domain->triclinic; - double old_xprd = domain->xprd; - double old_yprd = domain->yprd; - double old_zprd = domain->zprd; + old_xprd = domain->xprd; + old_yprd = domain->yprd; + old_zprd = domain->zprd; for (i = 0; i < 3; i++) { old_prd_half[i] = domain->prd_half[i]; old_center[i] = 0.5*(domain->boxlo[i]+domain->boxhi[i]); } - double old_xy = domain->xy; - double old_xz = domain->xz; - double old_yz = domain->yz; + old_xy = domain->xy; + old_xz = domain->xz; + old_yz = domain->yz; - // setup new simulation box + // define new simulation box domain->boxhi[0] = domain->boxlo[0] + nx*old_xprd; domain->boxhi[1] = domain->boxlo[1] + ny*old_yprd; @@ -280,15 +297,14 @@ void Replicate::command(int narg, char **arg) domain->yz *= nz; } - // new problem setup using new box boundaries + // setup of new system using new atom counts and new box boundaries + // allocate atom arrays to size N, rounded up by AtomVec->DELTA if (nprocs == 1) n = static_cast (atom->natoms); else n = static_cast (LB_FACTOR * atom->natoms / nprocs); atom->allocate_type_arrays(); - // allocate atom arrays to size N, rounded up by AtomVec->DELTA - bigint nbig = n; nbig = atom->avec->roundup(nbig); n = static_cast (nbig); @@ -362,15 +378,23 @@ void Replicate::command(int narg, char **arg) } } - // loop over all procs - // if this iteration of loop is me: - // pack my unmapped atom data into buf - // bcast it to all other procs - // performs 3d replicate loop with while loop over atoms in buf - // x = new replicated position, remapped into simulation box - // unpack atom into new atom class from buf if I own it - // adjust tag, mol #, coord, topology info as needed + // use + if (!bbox_flag) { + replicate_by_proc(nx,ny,nz,sublo,subhi,buf); + } else { + replicate_by_bbox(nx,ny,nz,sublo,subhi,buf); + } + + + + + + + + + + /* AtomVec *old_avec = old->avec; AtomVec *avec = atom->avec; @@ -381,7 +405,7 @@ void Replicate::command(int narg, char **arg) double *coord; int tag_enable = atom->tag_enable; - if (bbox_flag || bondlist_flag) { + if (bbox_flag || bond_flag) { // allgather size of buf on each proc @@ -456,7 +480,7 @@ void Replicate::command(int narg, char **arg) // store x and tag for the whole system (before replication) - if (bondlist_flag) { + if (bond_flag) { memory->create(old_x,old->natoms,3,"replicate:old_x"); memory->create(old_tag,old->natoms,"replicate:old_tag"); @@ -668,13 +692,13 @@ void Replicate::command(int narg, char **arg) if (atom->molecular == Atom::MOLECULAR) { if (atom->avec->bonds_allow) for (j = 0; j < atom->num_bond[i]; j++) { - if (bondlist_flag) + if (bond_flag) newtag(atom0tag,atom->bond_atom[i][j]); else atom->bond_atom[i][j] += atom_offset; } if (atom->avec->angles_allow) for (j = 0; j < atom->num_angle[i]; j++) { - if (bondlist_flag) { + if (bond_flag) { newtag(atom0tag,atom->angle_atom1[i][j]); newtag(atom0tag,atom->angle_atom2[i][j]); newtag(atom0tag,atom->angle_atom3[i][j]); @@ -686,7 +710,7 @@ void Replicate::command(int narg, char **arg) } if (atom->avec->dihedrals_allow) for (j = 0; j < atom->num_dihedral[i]; j++) { - if (bondlist_flag) { + if (bond_flag) { newtag(atom0tag,atom->dihedral_atom1[i][j]); newtag(atom0tag,atom->dihedral_atom2[i][j]); newtag(atom0tag,atom->dihedral_atom3[i][j]); @@ -700,7 +724,7 @@ void Replicate::command(int narg, char **arg) } if (atom->avec->impropers_allow) for (j = 0; j < atom->num_improper[i]; j++) { - if (bondlist_flag) { + if (bond_flag) { newtag(atom0tag,atom->improper_atom1[i][j]); newtag(atom0tag,atom->improper_atom2[i][j]); newtag(atom0tag,atom->improper_atom3[i][j]); @@ -725,7 +749,7 @@ void Replicate::command(int narg, char **arg) memory->destroy(size_buf_rnk); memory->destroy(disp_buf_rnk); memory->destroy(buf_all); - if (bondlist_flag) { + if (bond_flag) { memory->destroy(old_x); memory->destroy(old_tag); } @@ -825,8 +849,14 @@ void Replicate::command(int narg, char **arg) } } } - } // if (bbox_flag || bondlist_flag) + } // if (bbox_flag || bond_flag) + */ + + + + + // free communication buffer and old atom class memory->destroy(buf); @@ -889,8 +919,511 @@ void Replicate::command(int narg, char **arg) } /* ---------------------------------------------------------------------- - find new tag for the atom 'atom2bond' bonded to atom 'atom0' - for bondlist option, useful for periodic loops or inconsistent image flags + simple replication algorithm, suitable for small proc count +------------------------------------------------------------------------- */ + +void Replicate::replicate_by_proc(int nx, int ny, int nz, + double *sublo, double *subhi, double *buf) +{ + int i,j,m,n; + int ix,iy,iz; + + int me = comm->me; + int nprocs = comm->nprocs; + int triclinic = domain->triclinic; + int tag_enable = atom->tag_enable; + + AtomVec *old_avec = old->avec; + AtomVec *avec = atom->avec; + + tagint atom_offset,mol_offset; + imageint image; + double x[3],lamda[3]; + double *coord; + + // loop over all procs + // if this iteration of loop is me: + // pack my unmapped atom data into buf + // bcast it to all other procs + + for (int iproc = 0; iproc < nprocs; iproc++) { + if (me == iproc) { + n = 0; + for (i = 0; i < old->nlocal; i++) n += old_avec->pack_restart(i,&buf[n]); + } + MPI_Bcast(&n,1,MPI_INT,iproc,world); + MPI_Bcast(buf,n,MPI_DOUBLE,iproc,world); + + for (ix = 0; ix < nx; ix++) { + for (iy = 0; iy < ny; iy++) { + for (iz = 0; iz < nz; iz++) { + + // while loop over one proc's atom list + // x = new replicated position, remapped into new simulation box + // if atom is within my new subdomain, unpack it into new atom class + // adjust tag, mol #, coord, topology info as needed + + m = 0; + while (m < n) { + image = ((imageint) IMGMAX << IMG2BITS) | + ((imageint) IMGMAX << IMGBITS) | IMGMAX; + if (triclinic == 0) { + x[0] = buf[m+1] + ix*old_xprd; + x[1] = buf[m+2] + iy*old_yprd; + x[2] = buf[m+3] + iz*old_zprd; + } else { + x[0] = buf[m+1] + ix*old_xprd + iy*old_xy + iz*old_xz; + x[1] = buf[m+2] + iy*old_yprd + iz*old_yz; + x[2] = buf[m+3] + iz*old_zprd; + } + domain->remap(x,image); + if (triclinic) { + domain->x2lamda(x,lamda); + coord = lamda; + } else coord = x; + + if (coord[0] >= sublo[0] && coord[0] < subhi[0] && + coord[1] >= sublo[1] && coord[1] < subhi[1] && + coord[2] >= sublo[2] && coord[2] < subhi[2]) { + + m += avec->unpack_restart(&buf[m]); + + i = atom->nlocal - 1; + if (tag_enable) atom_offset = iz*ny*nx*maxtag + iy*nx*maxtag + ix*maxtag; + else atom_offset = 0; + mol_offset = iz*ny*nx*maxmol + iy*nx*maxmol + ix*maxmol; + + atom->x[i][0] = x[0]; + atom->x[i][1] = x[1]; + atom->x[i][2] = x[2]; + + atom->tag[i] += atom_offset; + atom->image[i] = image; + + if (atom->molecular != Atom::ATOMIC) { + if (atom->molecule[i] > 0) + atom->molecule[i] += mol_offset; + if (atom->molecular == Atom::MOLECULAR) { + if (atom->avec->bonds_allow) + for (j = 0; j < atom->num_bond[i]; j++) + atom->bond_atom[i][j] += atom_offset; + if (atom->avec->angles_allow) + for (j = 0; j < atom->num_angle[i]; j++) { + atom->angle_atom1[i][j] += atom_offset; + atom->angle_atom2[i][j] += atom_offset; + atom->angle_atom3[i][j] += atom_offset; + } + if (atom->avec->dihedrals_allow) + for (j = 0; j < atom->num_dihedral[i]; j++) { + atom->dihedral_atom1[i][j] += atom_offset; + atom->dihedral_atom2[i][j] += atom_offset; + atom->dihedral_atom3[i][j] += atom_offset; + atom->dihedral_atom4[i][j] += atom_offset; + } + if (atom->avec->impropers_allow) + for (j = 0; j < atom->num_improper[i]; j++) { + atom->improper_atom1[i][j] += atom_offset; + atom->improper_atom2[i][j] += atom_offset; + atom->improper_atom3[i][j] += atom_offset; + atom->improper_atom4[i][j] += atom_offset; + } + } + } + } else m += static_cast (buf[m]); + } + } + } + } + } +} + +/* ---------------------------------------------------------------------- + more complex replication algorithm + uses bounding box of each proc's subdomain to avoid checking individual atoms + faster for large processor counts + required for bond/periodic option +------------------------------------------------------------------------- */ + +void Replicate::replicate_by_bbox(int nx, int ny, int nz, + double *sublo, double *subhi, double *buf) +{ + int i,j,m,n; + int ix,iy,iz; + + int me = comm->me; + int nprocs = comm->nprocs; + int triclinic = domain->triclinic; + int tag_enable = atom->tag_enable; + + AtomVec *old_avec = old->avec; + AtomVec *avec = atom->avec; + + tagint atom_offset,mol_offset,atom0tag; + imageint image; + double x[3],lamda[3]; + double *coord; + + // allgather size of buf on each proc + + n = 0; + for (i = 0; i < old->nlocal; i++) n += old_avec->pack_restart(i,&buf[n]); + + int * size_buf_rnk; + memory->create(size_buf_rnk, nprocs, "replicate:size_buf_rnk"); + + MPI_Allgather(&n, 1, MPI_INT, size_buf_rnk, 1, MPI_INT, world); + + // size of buf_all + + int size_buf_all = 0; + MPI_Allreduce(&n, &size_buf_all, 1, MPI_INT, MPI_SUM, world); + + if (me == 0) { + auto mesg = fmt::format(" bounding box image = ({} {} {}) " + "to ({} {} {})\n", + _imagelo[0],_imagelo[1],_imagelo[2], + _imagehi[0],_imagehi[1],_imagehi[2]); + mesg += fmt::format(" bounding box extra memory = {:.2f} MB\n", + (double)size_buf_all*sizeof(double)/1024/1024); + utils::logmesg(lmp,mesg); + } + + // rnk offsets + + int *disp_buf_rnk; + memory->create(disp_buf_rnk, nprocs, "replicate:disp_buf_rnk"); + disp_buf_rnk[0] = 0; + for (i = 1; i < nprocs; i++) + disp_buf_rnk[i] = disp_buf_rnk[i-1] + size_buf_rnk[i-1]; + + // allgather buf_all + + double *buf_all; + memory->create(buf_all, size_buf_all, "replicate:buf_all"); + + MPI_Allgatherv(buf,n,MPI_DOUBLE,buf_all,size_buf_rnk,disp_buf_rnk, + MPI_DOUBLE,world); + + // bounding box of original unwrapped system + + double _orig_lo[3], _orig_hi[3]; + if (triclinic) { + _orig_lo[0] = domain->boxlo[0] + + _imagelo[0] * old_xprd + _imagelo[1] * old_xy + _imagelo[2] * old_xz; + _orig_lo[1] = domain->boxlo[1] + + _imagelo[1] * old_yprd + _imagelo[2] * old_yz; + _orig_lo[2] = domain->boxlo[2] + _imagelo[2] * old_zprd; + + _orig_hi[0] = domain->boxlo[0] + + (_imagehi[0]+1) * old_xprd + + (_imagehi[1]+1) * old_xy + (_imagehi[2]+1) * old_xz; + _orig_hi[1] = domain->boxlo[1] + + (_imagehi[1]+1) * old_yprd + (_imagehi[2]+1) * old_yz; + _orig_hi[2] = domain->boxlo[2] + (_imagehi[2]+1) * old_zprd; + } else { + _orig_lo[0] = domain->boxlo[0] + _imagelo[0] * old_xprd; + _orig_lo[1] = domain->boxlo[1] + _imagelo[1] * old_yprd; + _orig_lo[2] = domain->boxlo[2] + _imagelo[2] * old_zprd; + + _orig_hi[0] = domain->boxlo[0] + (_imagehi[0]+1) * old_xprd; + _orig_hi[1] = domain->boxlo[1] + (_imagehi[1]+1) * old_yprd; + _orig_hi[2] = domain->boxlo[2] + (_imagehi[2]+1) * old_zprd; + } + + double _lo[3], _hi[3]; + + int num_replicas_added = 0; + + // if bond/periodic option + // store old_x and old_tag for the entire original system + + if (bond_flag) { + memory->create(old_x,old->natoms,3,"replicate:old_x"); + memory->create(old_tag,old->natoms,"replicate:old_tag"); + + i = m = 0; + while (m < size_buf_all) { + old_x[i][0] = buf_all[m+1]; + old_x[i][1] = buf_all[m+2]; + old_x[i][2] = buf_all[m+3]; + old_tag[i] = (tagint) ubuf(buf_all[m+4]).i; + old_map.insert({old_tag[i],i}); + m += static_cast (buf_all[m]); + i++; + } + } + + // replication loop + + for (ix = 0; ix < nx; ix++) { + for (iy = 0; iy < ny; iy++) { + for (iz = 0; iz < nz; iz++) { + + thisrep[0] = ix; + thisrep[1] = iy; + thisrep[2] = iz; + + // domain->remap() overwrites coordinates, so always recompute here + + if (triclinic) { + _lo[0] = _orig_lo[0] + ix * old_xprd + iy * old_xy + iz * old_xz; + _hi[0] = _orig_hi[0] + ix * old_xprd + iy * old_xy + iz * old_xz; + + _lo[1] = _orig_lo[1] + iy * old_yprd + iz * old_yz; + _hi[1] = _orig_hi[1] + iy * old_yprd + iz * old_yz; + + _lo[2] = _orig_lo[2] + iz * old_zprd; + _hi[2] = _orig_hi[2] + iz * old_zprd; + } else { + _lo[0] = _orig_lo[0] + ix * old_xprd; + _hi[0] = _orig_hi[0] + ix * old_xprd; + + _lo[1] = _orig_lo[1] + iy * old_yprd; + _hi[1] = _orig_hi[1] + iy * old_yprd; + + _lo[2] = _orig_lo[2] + iz * old_zprd; + _hi[2] = _orig_hi[2] + iz * old_zprd; + } + + // test if bounding box of shifted replica overlaps sub-domain of proc + // if not, then can skip testing of any individual atoms + + int xoverlap = 1; + int yoverlap = 1; + int zoverlap = 1; + if (triclinic) { + double _llo[3]; + domain->x2lamda(_lo,_llo); + double _lhi[3]; + domain->x2lamda(_hi,_lhi); + + if (_llo[0] > (subhi[0] - EPSILON) + || _lhi[0] < (sublo[0] + EPSILON) ) xoverlap = 0; + if (_llo[1] > (subhi[1] - EPSILON) + || _lhi[1] < (sublo[1] + EPSILON) ) yoverlap = 0; + if (_llo[2] > (subhi[2] - EPSILON) + || _lhi[2] < (sublo[2] + EPSILON) ) zoverlap = 0; + } else { + if (_lo[0] > (subhi[0] - EPSILON) + || _hi[0] < (sublo[0] + EPSILON) ) xoverlap = 0; + if (_lo[1] > (subhi[1] - EPSILON) + || _hi[1] < (sublo[1] + EPSILON) ) yoverlap = 0; + if (_lo[2] > (subhi[2] - EPSILON) + || _hi[2] < (sublo[2] + EPSILON) ) zoverlap = 0; + } + + int overlap = 0; + if (xoverlap && yoverlap && zoverlap) overlap = 1; + + // if no overlap, test if bounding box wrapped back into new system + + if (!overlap) { + + // wrap back into cell + + imageint imagelo = ((imageint) IMGMAX << IMG2BITS) | + ((imageint) IMGMAX << IMGBITS) | IMGMAX; + domain->remap(&(_lo[0]), imagelo); + int xboxlo = (imagelo & IMGMASK) - IMGMAX; + int yboxlo = (imagelo >> IMGBITS & IMGMASK) - IMGMAX; + int zboxlo = (imagelo >> IMG2BITS) - IMGMAX; + + imageint imagehi = ((imageint) IMGMAX << IMG2BITS) | + ((imageint) IMGMAX << IMGBITS) | IMGMAX; + domain->remap(&(_hi[0]), imagehi); + int xboxhi = (imagehi & IMGMASK) - IMGMAX; + int yboxhi = (imagehi >> IMGBITS & IMGMASK) - IMGMAX; + int zboxhi = (imagehi >> IMG2BITS) - IMGMAX; + + if (triclinic) { + double _llo[3]; + _llo[0] = _lo[0]; _llo[1] = _lo[1]; _llo[2] = _lo[2]; + domain->x2lamda(_llo,_lo); + + double _lhi[3]; + _lhi[0] = _hi[0]; _lhi[1] = _hi[1]; _lhi[2] = _hi[2]; + domain->x2lamda(_lhi,_hi); + } + + // test all fragments for any overlap; ok to include false positives + + int _xoverlap1 = 0; + int _xoverlap2 = 0; + if (!xoverlap) { + if (xboxlo < 0) { + _xoverlap1 = 1; + if (_lo[0] > (subhi[0] - EPSILON)) _xoverlap1 = 0; + } + + if (xboxhi > 0) { + _xoverlap2 = 1; + if (_hi[0] < (sublo[0] + EPSILON)) _xoverlap2 = 0; + } + + if (_xoverlap1 || _xoverlap2) xoverlap = 1; + } + + int _yoverlap1 = 0; + int _yoverlap2 = 0; + if (!yoverlap) { + if (yboxlo < 0) { + _yoverlap1 = 1; + if (_lo[1] > (subhi[1] - EPSILON)) _yoverlap1 = 0; + } + + if (yboxhi > 0) { + _yoverlap2 = 1; + if (_hi[1] < (sublo[1] + EPSILON)) _yoverlap2 = 0; + } + + if (_yoverlap1 || _yoverlap2) yoverlap = 1; + } + + + int _zoverlap1 = 0; + int _zoverlap2 = 0; + if (!zoverlap) { + if (zboxlo < 0) { + _zoverlap1 = 1; + if (_lo[2] > (subhi[2] - EPSILON)) _zoverlap1 = 0; + } + + if (zboxhi > 0) { + _zoverlap2 = 1; + if (_hi[2] < (sublo[2] + EPSILON)) _zoverlap2 = 0; + } + + if (_zoverlap1 || _zoverlap2) zoverlap = 1; + } + + // does either fragment overlap w/ sub-domain + + if (xoverlap && yoverlap && zoverlap) overlap = 1; + } + + // while loop over one proc's atom list + + if (overlap) { + num_replicas_added++; + + m = 0; + while (m < size_buf_all) { + image = ((imageint) IMGMAX << IMG2BITS) | + ((imageint) IMGMAX << IMGBITS) | IMGMAX; + if (triclinic == 0) { + x[0] = buf_all[m+1] + ix*old_xprd; + x[1] = buf_all[m+2] + iy*old_yprd; + x[2] = buf_all[m+3] + iz*old_zprd; + } else { + x[0] = buf_all[m+1] + ix*old_xprd + iy*old_xy + iz*old_xz; + x[1] = buf_all[m+2] + iy*old_yprd + iz*old_yz; + x[2] = buf_all[m+3] + iz*old_zprd; + } + domain->remap(x,image); + if (triclinic) { + domain->x2lamda(x,lamda); + coord = lamda; + } else coord = x; + + if (coord[0] >= sublo[0] && coord[0] < subhi[0] && + coord[1] >= sublo[1] && coord[1] < subhi[1] && + coord[2] >= sublo[2] && coord[2] < subhi[2]) { + + m += avec->unpack_restart(&buf_all[m]); + + i = atom->nlocal - 1; + if (tag_enable) + atom_offset = iz*ny*nx*maxtag + iy*nx*maxtag + ix*maxtag; + else atom_offset = 0; + mol_offset = iz*ny*nx*maxmol + iy*nx*maxmol + ix*maxmol; + + atom->x[i][0] = x[0]; + atom->x[i][1] = x[1]; + atom->x[i][2] = x[2]; + + atom0tag = atom->tag[i]; + atom->tag[i] += atom_offset; + atom->image[i] = image; + + if (atom->molecular != Atom::ATOMIC) { + if (atom->molecule[i] > 0) + atom->molecule[i] += mol_offset; + if (atom->molecular == Atom::MOLECULAR) { + if (atom->avec->bonds_allow) + for (j = 0; j < atom->num_bond[i]; j++) { + if (bond_flag) + newtag(atom0tag,atom->bond_atom[i][j]); + else atom->bond_atom[i][j] += atom_offset; + } + if (atom->avec->angles_allow) + for (j = 0; j < atom->num_angle[i]; j++) { + if (bond_flag) { + newtag(atom0tag,atom->angle_atom1[i][j]); + newtag(atom0tag,atom->angle_atom2[i][j]); + newtag(atom0tag,atom->angle_atom3[i][j]); + } else { + atom->angle_atom1[i][j] += atom_offset; + atom->angle_atom2[i][j] += atom_offset; + atom->angle_atom3[i][j] += atom_offset; + } + } + if (atom->avec->dihedrals_allow) + for (j = 0; j < atom->num_dihedral[i]; j++) { + if (bond_flag) { + newtag(atom0tag,atom->dihedral_atom1[i][j]); + newtag(atom0tag,atom->dihedral_atom2[i][j]); + newtag(atom0tag,atom->dihedral_atom3[i][j]); + newtag(atom0tag,atom->dihedral_atom4[i][j]); + } else { + atom->dihedral_atom1[i][j] += atom_offset; + atom->dihedral_atom2[i][j] += atom_offset; + atom->dihedral_atom3[i][j] += atom_offset; + atom->dihedral_atom4[i][j] += atom_offset; + } + } + if (atom->avec->impropers_allow) + for (j = 0; j < atom->num_improper[i]; j++) { + if (bond_flag) { + newtag(atom0tag,atom->improper_atom1[i][j]); + newtag(atom0tag,atom->improper_atom2[i][j]); + newtag(atom0tag,atom->improper_atom3[i][j]); + newtag(atom0tag,atom->improper_atom4[i][j]); + } else { + atom->improper_atom1[i][j] += atom_offset; + atom->improper_atom2[i][j] += atom_offset; + atom->improper_atom3[i][j] += atom_offset; + atom->improper_atom4[i][j] += atom_offset; + } + } + } + } + } else m += static_cast (buf_all[m]); + } + } + } + } + } + + memory->destroy(size_buf_rnk); + memory->destroy(disp_buf_rnk); + memory->destroy(buf_all); + if (bond_flag) { + memory->destroy(old_x); + memory->destroy(old_tag); + } + + int sum = 0; + MPI_Reduce(&num_replicas_added, &sum, 1, MPI_INT, MPI_SUM, 0, world); + double avg = (double) sum / nprocs; + if (me == 0) + utils::logmesg(lmp," average # of replicas added to proc = {:.2f} out " + "of {} ({:.2f}%)\n",avg,nx*ny*nz,avg/(nx*ny*nz)*100.0); +} + +/* ---------------------------------------------------------------------- + find new tag for atom 'atom2bond' bonded to atom 'atom0' + for bond/periodic option + useful for periodic loops or inconsistent image flags reassign bond if > old boxlength / 2 ------------------------------------------------------------------------- */ diff --git a/src/replicate.h b/src/replicate.h index ae314d6a82..3877d2d720 100644 --- a/src/replicate.h +++ b/src/replicate.h @@ -31,13 +31,27 @@ class Replicate : public Command { Replicate(class LAMMPS *); void command(int, char **) override; - private: - std::unordered_map old_map; +private: + int bbox_flag, bond_flag; + + class Atom *old; + + double old_xprd, old_yprd, old_zprd; + double old_xy, old_xz, old_yz; + + int _imagelo[3], _imagehi[3]; + double **old_x; double old_prd_half[3], old_center[3]; tagint *old_tag; - tagint maxtag; + tagint maxtag, maxmol; int thisrep[3], allnrep[3]; + + std::unordered_map old_map; + + void replicate_by_proc(int, int, int, double *, double *, double *); + void replicate_by_bbox(int, int, int, double *, double *, double *); + void newtag(tagint, tagint &); };